Changeset e138de for src/atom_bondedparticle.cpp

Timestamp:

Nov 4, 2009, 7:56:04 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

1614174, e5ad5c

Parents:

7326b2

Message:

Huge change from ofstream * (const) out --> Log().

• first shift was done via regular expressions
• then via error messages from the code
• note that class atom, class element and class molecule kept in parts their output stream, was they print to file.
• make check runs fine
• MISSING: Verbosity is not fixed for everything (i.e. if no endl; is present and next has Verbose(0) ...)

Signed-off-by: Frederik Heber <heber@…>

File:

• src/atom_bondedparticle.cpp (modified) (8 diffs)

src/atom_bondedparticle.cpp

@@ -11 +11 @@
 #include "element.hpp"
 #include "lists.hpp"
+#include "log.hpp"
 #include "verbose.hpp"
 
@@ -36 +37 @@
 {
   *file << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
-  //cout << Verbose(2) << "Storing: " << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << "." << endl;
+  //Log() << Verbose(2) << "Storing: " << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << "." << endl;
 };
 
 /** Prints all bonds of this atom with total degree.
- * \param *out stream to output to
- * \return true - \a *out present, false - \a *out is NULL
  */
-bool BondedParticle::OutputBondOfAtom(ofstream *out) const
+void BondedParticle::OutputBondOfAtom() const
 {
-  if (out != NULL) {
-    *out << Verbose(4) << "Atom " << Name << "/" << nr << " with " << ListOfBonds.size() << " bonds: ";
-    int TotalDegree = 0;
-    for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
-      *out << **Runner << "\t";
-      TotalDegree += (*Runner)->BondDegree;
-    }
-    *out << " -- TotalDegree: " << TotalDegree << endl;
-    return true;
-  } else
-    return false;
+  Log() << Verbose(4) << "Atom " << Name << "/" << nr << " with " << ListOfBonds.size() << " bonds: ";
+  int TotalDegree = 0;
+  for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
+    Log() << Verbose(0) << **Runner << "\t";
+    TotalDegree += (*Runner)->BondDegree;
+  }
+  Log() << Verbose(0) << " -- TotalDegree: " << TotalDegree << endl;
 };
 
@@ -80 +75 @@
       status = true;
     } else {
-      cout << Verbose(1) << "ERROR: " << *Binder << " does not contain " << *this << "." << endl;
+      Log() << Verbose(1) << "ERROR: " << *Binder << " does not contain " << *this << "." << endl;
     }
   } else {
-    cout << Verbose(1) << "ERROR: Binder is " << Binder << "." << endl;
+    Log() << Verbose(1) << "ERROR: Binder is " << Binder << "." << endl;
   }
   return status;
@@ -99 +94 @@
       status = true;
     } else {
-      cout << Verbose(1) << "ERROR: " << *Binder << " does not contain " << *this << "." << endl;
+      Log() << Verbose(1) << "ERROR: " << *Binder << " does not contain " << *this << "." << endl;
     }
   } else {
-    cout << Verbose(1) << "ERROR: Binder is " << Binder << "." << endl;
+    Log() << Verbose(1) << "ERROR: Binder is " << Binder << "." << endl;
   }
   return status;
@@ -118 +113 @@
  * \param *out output stream for debugging
  */
-int BondedParticle::CorrectBondDegree(ofstream *out)
+int BondedParticle::CorrectBondDegree()
 {
   int NoBonds = 0;
@@ -126 +121 @@
   bond *CandidateBond = NULL;
 
-  //*out << Verbose(3) << "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
+  //Log() << Verbose(3) << "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
   NoBonds = CountBonds();
   if ((int)(type->NoValenceOrbitals) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
@@ -132 +127 @@
       OtherWalker = (*Runner)->GetOtherAtom(this);
       OtherNoBonds = OtherWalker->CountBonds();
-      //*out << Verbose(3) << "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
+      //Log() << Verbose(3) << "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
       if ((int)(OtherWalker->type->NoValenceOrbitals) > NoBonds) { // check if possible candidate
         if ((CandidateBond == NULL) || (ListOfBonds.size() > OtherWalker->ListOfBonds.size())) { // pick the one with fewer number of bonds first
           CandidateBond = (*Runner);
-          //*out << Verbose(3) << "New candidate is " << *CandidateBond << "." << endl;
+          //Log() << Verbose(3) << "New candidate is " << *CandidateBond << "." << endl;
         }
       }
@@ -142 +137 @@
     if ((CandidateBond != NULL)) {
       CandidateBond->BondDegree++;
-      *out << Verbose(2) << "Increased bond degree for bond " << *CandidateBond << "." << endl;
+      Log() << Verbose(2) << "Increased bond degree for bond " << *CandidateBond << "." << endl;
     } else {
-      //*out << Verbose(2) << "Could not find correct degree for atom " << *this << "." << endl;
+      //Log() << Verbose(2) << "Could not find correct degree for atom " << *this << "." << endl;
       FalseBondDegree++;
     }